WikiPathways

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Welcome to WikiPathways BETA

WikiPathways is a database of biological pathways maintained by and for the scientific community.

Find Pathways

Search

Browse

Browse by species and category

You can search by:
  • Pathway name (Apoptosis)
  • Gene or protein name (p53)
  • Any page content (cancer)

Get Pathways

Download

Multiple formats and methods

Growth

New pathways added each month

Edit Pathways

Sandbox

Play with the editor tools

Check out the following pages:

For more information see our Help topics


Today's Featured Pathway

Fluoropyrimidine Activity (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/5/50/WP1601_92636.svg:
Status:1
Message:Exception in thread "main" java.lang.NullPointerException at org.pathvisio.core.Engine.getPathwayImporters(Unknown Source) at org.pathvisio.core.Engine.importPathway(Unknown Source) at org.pathvisio.core.util.Converter.main(Unknown Source)


Command:java -Xmx1024M -jar /var/www/wikipathways/wpi/bin/pathvisio_core.jar "/var/www/wikipathways" "/var/www/wikipathways/images/5/50/WP1601_92636.svg" 2>&1
' in /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php:1255 Stack trace:

  1. 0 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1227): Pathway::convertWithPathVisio(false, '/var/www/wikipa...')
  2. 1 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1137): Pathway->saveConvertedByPathVisioCache('svg')
  3. 2 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1153): Pathway->updateCache('svg')
  4. 3 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(129): Pathway->getImage()
  5. 4 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(53): makeThumbLinkObj(Object(Pathway), 'Fluoropyrimidin...', 'https://www.wik...', 'Fluoropyrimidin...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP1601', '300', 'center', 'Fluoropyrimidin...', 'pathway', 'Fluoropyrimidin...')
  7. 6 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('renderPathwayIm...', Array)
  8. 7 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  9. 8 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  10. 9 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  11. 10 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  12. 11 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{Template:Toda...')
  13. 12 /var/www/wikipathways/includes/parser/Parser.php(439): Parser->internalParse('{{Template:Toda...')
  14. 13 /var/www/wikipathways/wpi/extensions/PathwayOfTheDay/PathwayOfTheDay.php(60): Parser->recursiveTagParse('{{Template:Toda...')
  15. 14 [internal function]: getPathwayOfTheDay(Object(Parser), 'Wednesday 5 Aug...', 'Curation:Featur...', 'true')
  16. 15 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('getPathwayOfThe...', Array)
  17. 16 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  18. 17 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  19. 18 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('__NOEDITSECTION...')
  20. 19 /var/www/wikipathways/includes/parser/Parser.php(321): Parser->internalParse('__NOEDITSECTION...')
  21. 20 /var/www/wikipathways/includes/Article.php(3406): Parser->parse('__NOEDITSECTION...', Object(Title), Object(ParserOptions), true, true, 92636)
  22. 21 /var/www/wikipathways/includes/Article.php(875): Article->outputWikiText('__NOEDITSECTION...', false)
  23. 22 /var/www/wikipathways/includes/Wiki.php(437): Article->view()
  24. 23 /var/www/wikipathways/includes/Wiki.php(59): MediaWiki->performAction(Object(OutputPage), Object(Article), Object(Title), Object(User), Object(WebRequest))
  25. 24 /var/www/wikipathways/index.php(93): MediaWiki->initialize(Object(Title), Object(Article), Object(OutputPage), Object(User), Object(WebRequest))
  26. 25 {main}

Updates

  • June 2017 Release: 124 edits by 21 contributors, and 6 new pathways this month
  • April 2017 Release: 80 edits by 8 contributors this month
  • March 2017 Release: 54 edits by 10 contributors this month
  • February 2017 Release: 56 edits by 8 contributors this month
  • February 2: Rett syndrome pathway is now live at Wikipedia
  • January 2017 Release: 25 new human pathways with 181 new genes
  • December 22: Blog post about our translation of mouse pathways
  • December 2016 Release: 201 edits by 15 contributors this month
  • November 11: Enrichment analysis of single-cell dataset on differentiation
  • November 2016 Release: 143 new human genes added to pathways
  • October 2016 Release: 12 new human pathways contributed
  • Sept 30: New pathways featured in blog post
  • September 2016 Release: 42 new human genes added
  • August 2016 Release: 60 genes and 10 new human pathways added
  • Want to add your ORCID id to your WikiPathways account? Learn how

Discussions

Today
Welcome! (20) by Marvin Martens
6 July 2020
MRE11A with mouse gene annotation (1) by Egon Willighagen
    more...

Forum

  Re: [wp-discuss] add annotations to svg elements using data tags
Thanks for the info, I will play around with them. Btw, I have found a programmatically more convenient and dynamic way of adding the metadata to the SVGs: ?]
  Re: [wp-discuss] Gene Symbol Aliases Problem
Dear Phil, So in WikiPathways, every data node has a label and an identifier. For searches like you want, I would always advise to use the identifier search and not by text / label. For human genes, you can actually use the official gene symbols (HGNC) since we have an integrated identifier [?]
  Re: [wp-discuss] Gene Symbol Aliases Problem
Dear Tina, Thanks for your quick response. The current issue is that Wikipathways does not require the use of the official gene symbols (HGNC) for datanodes in pathways. This can result in a datanode using an alias instead of an official gene symbol which would result in cases where not all [?]
  Re: [wp-discuss] Unable to connect to wikipathways
Hi, WikiPathways is up and running and I just successfully tested the connection via the plugin in PathVisio. This is an intermittent problem that we see sometimes. Please wait a while and try again. Regards, Kristina On Mon, Jul 20, 2020 at 10:47 AM wrote: > I have [?]
  Re: [wp-discuss] Mapping database
Thank you so much..... Got the point [?]
  Unable to connect to wikipathways
I have been using pathvisio for the past week, and, all of a sudden at some point today, I have no longer been able to connect to wikipathways when I click on the plugin. Has something changed? I have tried restarting pathvisio and my computer, but I get the same error message: "Connection [?]
  Re: [wp-discuss] Gene Symbol Aliases Problem
Dear Phil, I'll look into this issue and check if you can do an actual identifier search using the search field on the website (I think so but I am uncertain of the syntax right now). Currently, you are using the free text search available on the website, which is looking for the text in the [?]
  Gene Symbol Aliases Problem
Hi, Sorry if this is an issue that has been discussed before. There seems to be an issue when you search on a gene symbol (e.g. IL6 versus IL-6). Both gene symbols return two different sets of pathways but since they are they are aliases of each other they should return all of the same (a [?]
  Re: [wp-discuss] Wikipathway Widget xref recognition
Hi Jakob, We have another version of the viewer in development. It maps gene product identifiers to all of the following: Ensembl, Entrez (NCBI) Gene, HGNC and Wikidata. If you'd like to specify just Ensembl identifiers, you can do so like this (note the underscores): https://pathway-viewer.too [?]
  Re: [wp-discuss] Wikipathway Widget xref recognition
Dear Egon, thank you very much for your message! I am now using a method previously suggested in this group by first creating a mapping table from GraphIds to UniProt, Ensembl, and Gene Id, and then calling the widget with the GraphIds. This works reasonably well. It would still be nice to have [?]
  Re: [wp-discuss] Wikipathway Widget xref recognition
Dear Jakob, all (developers, see my question at the end), On Wed, Jul 8, 2020 at 8:56 PM wrote: > I have started using your excellent Widget for displaying protein fold > change color-coded on the pathways. This in principle works great, but > there is an issue with [?]
  Re: [wp-discuss] Re: Installing Pathvisio APPs
Dear Meghan, I am still working on moving some of the plugin documentation over. Sorry about that. The MAPPBuilder plugin can be used to create annotated data nodes from a list of genes. So if you have a table with gene names and identifiers, you only need to add the system code column indicatin [?]
  Re: [wp-discuss] Mapping database
Hi, If you check the instructions here: https://pathvisio.github.io/tutorials/getting-started.html, you find a section on "Select an Identifier Mapping Database". If you follow the instructions, you should be able to search for gene products and metabolites when you have the .bridge files [?]
  Wikipathway Widget xref recognition
Dear team, I have started using your excellent Widget for displaying protein fold change color-coded on the pathways. This in principle works great, but there is an issue with consistency of xrefs that somehow limits usability. As far as I understand colors are only displayed when the xref given [?]
  Mapping database
I have newly installed pathvisio and some of its plugins but everytime I try to search for gene product or metabolite it shows that no identifier mapping database loaded. Please tell me what is the problem. Thanks [?]
    Google group wikipathways-discuss
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